I have Sonar X1 clock synced as MIDI slave. After hitting play on the external controller, it starts fine. But the problem is that it bypasses the clip(s) I have set to loop. How do I get Sonar to loop the selected clip(s) when it's in midi sync slave mode? Any help is much appreciated.

AFAIK you can't. If Sonar is the slave then it's getting clock information from the external device so unless the external device is telling Sonar to loop it won't.

What are you trying to do? There may well be a way to do it without Sonar as slave.

Try making Sonar the master and the other device the slave. 

Well, I'm sequencing Sonar instruments with the Roland MC-303. I don't like programming on piano roll much, so the mc303 is better for me. So far it's working good. But, I just wish i could make a sequencer clip (controlling an external synthesizer) loop on Sonar, and then, mute/unmute that part (midi channel) with the mc303.